title: In silico microarray probe design for diagnosis of multiple pathogens.
abstract: BACKGROUND
  With multiple strains of various pathogens being sequenced, it is necessary to develop high-throughput methods that can simultaneously process multiple bacterial or viral genomes to find common fingerprints as well as fingerprints that are unique to each individual genome. We present algorithmic enhancements to an existing single-genome pipeline that allows for efficient design of microarray probes common to groups of target genomes. The enhanced pipeline takes advantage of the similarities in the input genomes to narrow the search to short, nonredundant regions of the target genomes and, thereby, significantly reduces the computation time. The pipeline also computes a three-state hybridization matrix, which gives the expected hybridization of each probe with each target.
  
  
  RESULTS
  Design of microarray probes for eight pathogenic Burkholderia genomes shows that the multiple-genome pipeline is nearly four-times faster than the single-genome pipeline for this application. The probes designed for these eight genomes were experimentally tested with one non-target and three target genomes. Hybridization experiments show that less than 10% of the designed probes cross hybridize with non-targets. Also, more than 65% of the probes designed to identify all Burkholderia mallei and B. pseudomallei strains successfully hybridize with a B. pseudomallei strain not used for probe design.
  
  
  CONCLUSIONS
  The savings in runtime suggest that the enhanced pipeline can be used to design fingerprints for tens or even hundreds of related genomes in a single run. Hybridization results with an unsequenced B. pseudomallei strain indicate that the designed probes might be useful in identifying unsequenced strains of B. mallei and B. pseudomallei.
authors.affiliation: Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA. rvijaya@bioanalysis.org
authors.forename: Ravi
authors.initials: R
authors.lastname: Vijaya Satya
authors.forename: Nela
authors.initials: N
authors.lastname: Zavaljevski
authors.forename: Kamal
authors.initials: K
authors.lastname: Kumar
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Bode
authors.forename: Susana
authors.initials: S
authors.lastname: Padilla
authors.forename: Leonard
authors.initials: L
authors.lastname: Wasieloski
authors.forename: Jeanne
authors.initials: J
authors.lastname: Geyer
authors.forename: Jaques
authors.initials: J
authors.lastname: Reifman
mesh_terms: D000465:Algorithms; D015373:Bacterial Typing Techniques; D019117:Burkholderia / Q000145:classification / Q000235:genetics*; D019295:Computational Biology; D016172:DNA Fingerprinting / Q000379:methods*; D015342:DNA Probes; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
chemical_list: D015342:DNA Probes; D004269:DNA, Bacterial